@weng-lab/genomebrowser-ui 0.2.4 → 0.2.6

package/src/TrackSelect/Folders/biosamples/data/mark_core.go

@@ -0,0 +1,158 @@
+//go:build ignore
+
+package main
+
+import (
+	"bufio"
+	"encoding/json"
+	"fmt"
+	"os"
+	"regexp"
+	"strings"
+)
+
+type Assay struct {
+	ID                  string `json:"id"`
+	Assay               string `json:"assay"`
+	URL                 string `json:"url"`
+	ExperimentAccession string `json:"experimentAccession"`
+	FileAccession       string `json:"fileAccession"`
+}
+
+type Track struct {
+	Name        string  `json:"name"`
+	Core        bool    `json:"core,omitempty"`
+	Ontology    string  `json:"ontology"`
+	LifeStage   string  `json:"lifeStage"`
+	SampleType  string  `json:"sampleType"`
+	DisplayName string  `json:"displayName"`
+	Assays      []Assay `json:"assays"`
+}
+
+type BiosampleData struct {
+	Tracks []Track `json:"tracks"`
+}
+
+// CoreSample represents a sample to be marked as core, with donor ID and display name
+type CoreSample struct {
+	DonorID     string
+	DisplayName string
+}
+
+func main() {
+	// Extract core samples from test.txt (donor ID + display name pairs)
+	coreSamples, err := extractCoreSamples("test.txt")
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error reading test.txt: %v\n", err)
+		os.Exit(1)
+	}
+	fmt.Printf("Found %d core samples to mark\n", len(coreSamples))
+
+	// Load human.json
+	data, err := os.ReadFile("human.json")
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error reading human.json: %v\n", err)
+		os.Exit(1)
+	}
+
+	var biosampleData BiosampleData
+	if err := json.Unmarshal(data, &biosampleData); err != nil {
+		fmt.Fprintf(os.Stderr, "Error parsing human.json: %v\n", err)
+		os.Exit(1)
+	}
+	fmt.Printf("Loaded %d tracks\n", len(biosampleData.Tracks))
+
+	// Mark tracks as core if they match both donor ID and display name
+	markedCount := 0
+	alreadyCore := 0
+	for i := range biosampleData.Tracks {
+		track := &biosampleData.Tracks[i]
+		for _, sample := range coreSamples {
+			// Check if track name ends with the donor ID AND display name matches (case-insensitive)
+			if strings.HasSuffix(track.Name, "_"+sample.DonorID) &&
+				strings.EqualFold(track.DisplayName, sample.DisplayName) {
+				if track.Core {
+					alreadyCore++
+				} else {
+					track.Core = true
+					markedCount++
+				}
+				break
+			}
+		}
+	}
+	fmt.Printf("Marked %d tracks as core (already core: %d)\n", markedCount, alreadyCore)
+
+	// Write to temp file
+	output, err := json.MarshalIndent(biosampleData, "", "  ")
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Error marshaling JSON: %v\n", err)
+		os.Exit(1)
+	}
+
+	if err := os.WriteFile("human_updated.json", output, 0644); err != nil {
+		fmt.Fprintf(os.Stderr, "Error writing human_updated.json: %v\n", err)
+		os.Exit(1)
+	}
+	fmt.Println("Wrote updated data to human_updated.json")
+}
+
+// extractCoreSamples parses test.txt and extracts donor ID + display name pairs
+// Format: "Organ \t Type \t ENCDO... \t DisplayName: (1) cCREs \t Data format"
+func extractCoreSamples(filename string) ([]CoreSample, error) {
+	file, err := os.Open(filename)
+	if err != nil {
+		return nil, err
+	}
+	defer file.Close()
+
+	var samples []CoreSample
+	donorRe := regexp.MustCompile(`ENCDO\w+`)
+
+	scanner := bufio.NewScanner(file)
+	for scanner.Scan() {
+		line := scanner.Text()
+		if strings.TrimSpace(line) == "" {
+			continue
+		}
+
+		// Find the donor ID
+		donorMatch := donorRe.FindString(line)
+		if donorMatch == "" {
+			continue
+		}
+
+		// Extract display name: it's after the donor ID, before ": (1)"
+		// Split by donor ID to get the part after it
+		parts := strings.SplitN(line, donorMatch, 2)
+		if len(parts) < 2 {
+			continue
+		}
+
+		afterDonor := parts[1]
+		// Remove leading tab/whitespace
+		afterDonor = strings.TrimLeft(afterDonor, " \t")
+
+		// Extract the display name (before ": (1)" or ":(1)")
+		displayName := afterDonor
+		if idx := strings.Index(afterDonor, ": ("); idx != -1 {
+			displayName = afterDonor[:idx]
+		} else if idx := strings.Index(afterDonor, ":("); idx != -1 {
+			displayName = afterDonor[:idx]
+		}
+
+		displayName = strings.TrimSpace(displayName)
+		if displayName != "" {
+			samples = append(samples, CoreSample{
+				DonorID:     donorMatch,
+				DisplayName: displayName,
+			})
+		}
+	}
+
+	if err := scanner.Err(); err != nil {
+		return nil, err
+	}
+
+	return samples, nil
+}

package/src/TrackSelect/Folders/biosamples/shared/columns.tsx

@@ -1,8 +1,42 @@
-import { GridColDef } from "@mui/x-data-grid-premium";
+import {
+  GridColDef,
+  GridRenderCellParams,
+  GridGroupNode,
+  useGridApiContext,
+} from "@mui/x-data-grid-premium";
 import { Stack, capitalize } from "@mui/material";
-import { AssayIcon, ontologyTypes, assayTypes } from "./constants";
+import Check from "@mui/icons-material/Check";
+import { AssayIcon, ontologyTypes, assayTypes, lifeStages } from "./constants";
 import { BiosampleRowInfo } from "./types";
 
+function CoreCollectionCell(params: GridRenderCellParams<BiosampleRowInfo>) {
+  const apiRef = useGridApiContext();
+
+  if (params.rowNode.type !== "group") {
+    return null;
+  }
+
+  const groupNode = params.rowNode as GridGroupNode;
+  if (groupNode.groupingField !== "displayName") {
+    return null;
+  }
+
+  const childIds = groupNode.children;
+  if (!childIds || childIds.length === 0) {
+    return null;
+  }
+
+  const firstChildRow = apiRef.current.getRow(
+    childIds[0],
+  ) as BiosampleRowInfo | null;
+
+  if (firstChildRow?.coreCollection) {
+    return <Check color="primary" />;
+  }
+
+  return null;
+}
+
 const displayNameCol: GridColDef<BiosampleRowInfo> = {
   field: "displayName",
   headerName: "Name",
@@ -94,14 +128,7 @@ const sampleTypeCol: GridColDef<BiosampleRowInfo> = {
   field: "sampleType",
   headerName: "Sample Type",
   type: "singleSelect",
-  valueOptions: [
-    "Aggregate",
-    "Tissue",
-    "Primary cell",
-    "Cell line",
-    "In vitro differentiated cells",
-    "Organoid",
-  ],
+  valueOptions: ontologyTypes,
   valueFormatter: (value) => value && capitalize(value),
 };
 
@@ -109,10 +136,18 @@ const lifeStageCol: GridColDef<BiosampleRowInfo> = {
   field: "lifeStage",
   headerName: "Life Stage",
   type: "singleSelect",
-  valueOptions: ["Adult", "Embryonic", "N/A"],
+  valueOptions: lifeStages,
   valueFormatter: (value) => value && capitalize(value),
 };
 
+const coreCollectionCol: GridColDef<BiosampleRowInfo> = {
+  field: "coreCollection",
+  headerName: "Core Collection",
+  type: "boolean",
+  width: 120,
+  renderCell: (params) => <CoreCollectionCell {...params} />,
+};
+
 const experimentCol: GridColDef<BiosampleRowInfo> = {
   field: "experimentAccession",
   headerName: "Experiment Accession",
@@ -132,6 +167,7 @@ const idCol: GridColDef<BiosampleRowInfo> = {
 export const sortedByAssayColumns: GridColDef<BiosampleRowInfo>[] = [
   displayNameCol,
   sortedByAssayOntologyCol,
+  coreCollectionCol,
   sampleTypeCol,
   lifeStageCol,
   sortedByAssayAssayCol,
@@ -143,6 +179,7 @@ export const sortedByAssayColumns: GridColDef<BiosampleRowInfo>[] = [
 /** Default columns (ontology as top-level grouping) */
 export const defaultColumns: GridColDef<BiosampleRowInfo>[] = [
   defaultAssayCol,
+  coreCollectionCol,
   sampleTypeCol,
   lifeStageCol,
   defaultOntologyCol,

package/src/TrackSelect/Folders/biosamples/shared/constants.tsx

@@ -14,6 +14,8 @@ export const assayTypes = [
   "ChromHMM",
 ];
 
+export const lifeStages = ["Adult", "Embryonic", "N/A"];
+
 export const ontologyTypes = [
   "Aggregate",
   "Adipose",

package/src/TrackSelect/Folders/biosamples/shared/createFolder.ts

@@ -24,9 +24,18 @@ import { BiosampleTreeItem } from "./BiosampleTreeItem";
  * @returns Array of flattened BiosampleRowInfo objects, one per assay
  */
 function flattenTrackIntoRows(track: BiosampleTrackInfo): BiosampleRowInfo[] {
-  const { ontology, lifeStage, sampleType, displayName } = track;
+  const { ontology, lifeStage, sampleType, displayName, core } = track;
 
-  return track.assays.map(
+  // Sort assays so cCRE comes first, then maintain original order for the rest
+  const sortedAssays = [...track.assays].sort((a, b) => {
+    const aIsCcre = a.assay.toLowerCase() === "ccre";
+    const bIsCcre = b.assay.toLowerCase() === "ccre";
+    if (aIsCcre && !bIsCcre) return -1;
+    if (!aIsCcre && bIsCcre) return 1;
+    return 0;
+  });
+
+  return sortedAssays.map(
     ({ id, assay, experimentAccession, fileAccession, url }) => ({
       id,
       ontology: capitalize(ontology),
@@ -37,6 +46,7 @@ function flattenTrackIntoRows(track: BiosampleTrackInfo): BiosampleRowInfo[] {
       experimentAccession,
       fileAccession,
       url,
+      coreCollection: core ?? false,
     }),
   );
 }

package/src/TrackSelect/Folders/biosamples/shared/types.ts

@@ -23,6 +23,7 @@ export type BiosampleTrackInfo = {
   sampleType: string;
   displayName: string;
   assays: BiosampleAssayInfo[];
+  core?: boolean;
 };
 
 /**
@@ -38,6 +39,7 @@ export type BiosampleRowInfo = {
   experimentAccession: string;
   fileAccession: string;
   url: string;
+  coreCollection: boolean;
 };
 
 /**

package/test/main.tsx

@@ -79,7 +79,7 @@ function injectCallbacks(track: Track, callbacks: TrackCallbacks): Track {
 
 function Main() {
   const [open, setOpen] = useState(false);
-  const currentAssembly: Assembly = "mm10";
+  const currentAssembly: Assembly = "GRCh38";
 
   const browserStore = createBrowserStoreMemo({
     // chr7:19,695,494-19,699,803